Hi Maite,
In addition, you should be careful with G53a*. Beware that atom
bond/angle/dihedral type definitions have changed. If these are
referenced by a number (gb_/ga_/gd_) then you have to check each one
of them. Also, it appears that the G53a* force fields have problems
with the backbone dihedral terms, resulting in a destabilization of
helices and more. No references on that yet, but the differences
between the new and the previous GROMOS force fields (53a5/53a6/43a2)
will be discussed in a soon-to-appear paper in JPCB (I think it was
B...). You might want to stick to 43a2...
Best,
Tsjerk
On 4/4/07, Chris Neale <[EMAIL PROTECTED]> wrote:
As mentioned by another user, you need POPC in the [ molecules ]
section. In addition, I see a lack of reference to popc.itp in yout .top
file. If it is truely absent, this next bit is important.
You have referenced this link:
1) http://www.gromacs.org/pipermail/gmx-users/2006-September/023639.html
and that page includes a link to:
2) http://www.gromacs.org/pipermail/gmx-users/2006-May/021416.html
and that link includes the following information:
######################
4. make a topology file like this:
#include "ffoplsaa.itp"
#include "myprotein.itp"
#include "spc.itp"
#include "pope.itp"
[ system ]
system_name
[ molecules ]
; Compound #mols
Protein 1
POPE 299
SOL 8991
######################
But your email doesn't mention popc.itp. Download that file and include it.
If you did miss that bit then I would recommend going back through the
instructions to see if you missed something else as well.
Also, I would at least think about doing something like this:
http://www.gromacs.org/pipermail/gmx-users/2006-September/023761.html
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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